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Book ; Conference proceedings: DNA protein interactions in transcription

Gralla, Jay D.

proceedings of Director's Sponsors UCLA Symposium [Titled DNA-Protein Complexes in Transcription], held at Keystone, Colorado, April 4 - 10, 1988

(UCLA Symposia on Molecular and Cellular Biology ; N.s., 95)

1989

Title variant	DNA-protein
Institution	Symposium Titled DNA Protein Complexes in Transcription
Author's details	ed. Jay D. Gralla
Series title	UCLA Symposia on Molecular and Cellular Biology ; N.s., 95
Collection
Keywords	Transcription, Genetic / congresses ; Transcription Factors / congresses ; Eukaryoten ; Transkription ; Prokaryoten ; DNS ; Proteine ; Wechselwirkung
Subject	Wechselwirkungen ; Interaktion ; Eiweiss ; Protein ; Desoxyribonucleinsäure ; DNA ; DNA-Molekül ; Desoxyribonukleinsäure ; Prokaryonten ; Protokaryonten ; Prokaryota ; Prokarya ; Procaryota ; Procarya ; Monera ; Anukleobionten ; Akaryobionten ; Eukaryonten ; Eukaryota ; Eukarya ; Eucaryota ; Eucarya ; Nukleobionten
Language	English
Size	XVII, 333 S. : Ill., graph. Darst.
Publisher	Liss
Publishing place	New York
Publishing country	United States
Document type	Book ; Conference proceedings
HBZ-ID	HT003418320
ISBN	0-8451-2694-6 ; 978-0-8451-2694-3
Database	Catalogue ZB MED Medicine, Health

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Article: Escherichia coli ribosomal RNA transcription: regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein.

Gralla, Jay D

Molecular microbiology

2005 Volume 55, Issue 4, Page(s) 973–977

Abstract: Ribosomal RNA transcription can limit the rate of Escherichia coli growth and is subject to complex regulation. Somehow, the cell is able to sense the general nutritional environment and adjust rRNA transcription so that an appropriate number of ... ...

Abstract	Ribosomal RNA transcription can limit the rate of Escherichia coli growth and is subject to complex regulation. Somehow, the cell is able to sense the general nutritional environment and adjust rRNA transcription so that an appropriate number of ribosomes is produced. This review discusses the current state of affairs, including recent information about the involvement of two nucleotide regulators, two architectural protein regulators, one new co-regulator and stalled ribosomes.
MeSH term(s)	Bacterial Proteins/metabolism ; Escherichia coli/genetics ; Gene Expression Regulation, Bacterial ; Guanosine Tetraphosphate/metabolism ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; Transcription, Genetic
Chemical Substances	Bacterial Proteins ; RNA, Bacterial ; RNA, Ribosomal ; Guanosine Tetraphosphate (33503-72-9)
Language	English
Publishing date	2005-02
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S. ; Review
ZDB-ID	619315-8
ISSN	1365-2958 ; 0950-382X
ISSN (online)	1365-2958
ISSN	0950-382X
DOI	10.1111/j.1365-2958.2004.04455.x
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Article ; Online: The TFIIB tip domain couples transcription initiation to events involved in RNA processing.

Tran, Khiem / Gralla, Jay D

The Journal of biological chemistry

2010 Volume 285, Issue 51, Page(s) 39580–39587

Abstract: TFIIB is the only factor within the multimegadalton transcription complex that is obligatorily required to undergo dissociation and re-association with each round of mRNA transcription. Here we show that a six-amino acid human TFIIB tip region is needed ... ...

Abstract	TFIIB is the only factor within the multimegadalton transcription complex that is obligatorily required to undergo dissociation and re-association with each round of mRNA transcription. Here we show that a six-amino acid human TFIIB tip region is needed for appropriate levels of serine 5 C-terminal domain phosphorylation and mRNA capping and for retention of the required elongation factor TFIIF. We suggest that the broad functions of this tiny region are used to suppress transcription noise by restricting functional RNA synthesis from non-promoter sites on the genome, which will not contain TFIIB.
MeSH term(s)	HeLa Cells ; Humans ; RNA Caps/genetics ; RNA Caps/metabolism ; RNA Processing, Post-Transcriptional/physiology ; RNA, Fungal/biosynthesis ; RNA, Fungal/genetics ; Schizosaccharomyces/genetics ; Schizosaccharomyces/metabolism ; Schizosaccharomyces pombe Proteins/genetics ; Schizosaccharomyces pombe Proteins/metabolism ; Transcription Factor TFIIB/genetics ; Transcription Factor TFIIB/metabolism ; Transcription Factors, TFII/genetics ; Transcription Factors, TFII/metabolism ; Transcription, Genetic/physiology ; Transcriptional Activation/physiology
Chemical Substances	RNA Caps ; RNA, Fungal ; Schizosaccharomyces pombe Proteins ; Transcription Factor TFIIB ; Transcription Factors, TFII ; transcription factor TFIIF (EC 3.6.4.12)
Language	English
Publishing date	2010-09-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M110.171850
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Article: The TFIIB Tip Domain Couples Transcription Initiation to Events Involved in RNA Processing

Tran, Khiem / Gralla, Jay D

Journal of biological chemistry. 2010 Dec. 17, v. 285, no. 51

2010

Abstract	TFIIB is the only factor within the multimegadalton transcription complex that is obligatorily required to undergo dissociation and re-association with each round of mRNA transcription. Here we show that a six-amino acid human TFIIB tip region is needed for appropriate levels of serine 5 C-terminal domain phosphorylation and mRNA capping and for retention of the required elongation factor TFIIF. We suggest that the broad functions of this tiny region are used to suppress transcription noise by restricting functional RNA synthesis from non-promoter sites on the genome, which will not contain TFIIB.
Language	English
Dates of publication	2010-1217
Size	p. 39580-39587.
Publishing place	American Society for Biochemistry and Molecular Biology
Document type	Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
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Article: Control of the timing of promoter escape and RNA catalysis by the transcription factor IIb fingertip.

Tran, Khiem / Gralla, Jay D

The Journal of biological chemistry

2008 Volume 283, Issue 23, Page(s) 15665–15671

Abstract: Transcription factor IIB (TFIIB) recruits RNA polymerase II to promoters and inserts a finger domain into its active site, with unknown consequences. Here we show that that the tip of this finger is important for two transcription initiation functions. ... ...

Abstract	Transcription factor IIB (TFIIB) recruits RNA polymerase II to promoters and inserts a finger domain into its active site, with unknown consequences. Here we show that that the tip of this finger is important for two transcription initiation functions. First, TFIIB acts as a catalytic cofactor for initial RNA bond formation. It does so via a pair of fingertip aspartates that can bind magnesium, placing TFIIB within a family of proteins that insert finger domains to alter the catalytic functions of RNA polymerase. Second, the TFIIB fingertip mediates the timing of the release of TFIIB that is associated with appropriate promoter escape. These initiation requirements may assist in RNA quality control by minimizing functional synthesis when RNA polymerase becomes inappropriately associated with the genome without having been recruited there by TFIIB.
MeSH term(s)	Catalysis ; Genome, Human/physiology ; Humans ; Promoter Regions, Genetic/physiology ; Protein Structure, Tertiary/physiology ; RNA Polymerase II/chemistry ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; RNA, Messenger/biosynthesis ; RNA, Messenger/chemistry ; RNA, Messenger/genetics ; Transcription Factor TFIIB/chemistry ; Transcription Factor TFIIB/genetics ; Transcription Factor TFIIB/metabolism
Chemical Substances	RNA, Messenger ; Transcription Factor TFIIB ; RNA Polymerase II (EC 2.7.7.-)
Language	English
Publishing date	2008-04-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M801439200
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Article ; Online: Remodeling and activation of Escherichia coli RNA polymerase by osmolytes.

Gralla, Jay D / Huo, Yi-Xin

Biochemistry

2008 Volume 47, Issue 50, Page(s) 13189–13196

Abstract: The ability of bacteria to survive environmental stresses and colonize the gastrointestinal tract depends on adaptation to high osmolarity. The adaptation involves global reprogramming of gene expression, including inhibition of bulk sigma70 RNA ... ...

Abstract	The ability of bacteria to survive environmental stresses and colonize the gastrointestinal tract depends on adaptation to high osmolarity. The adaptation involves global reprogramming of gene expression, including inhibition of bulk sigma70 RNA polymerase transcription and activation of bulk sigma38 transcription. The activating signal transduction pathways that originate with osmolytes remain to be established. Experiments here confirm that accumulation of a simple signaling molecule, glutamate, can reprogram RNA polymerase in vitro without the need for specific protein receptors. During osmotic activation, glutamate appears to act as a Hofmeister series osmolyte to facilitate promoter escape. Escape is accompanied by a remodeling of the key interaction between the sigma38 stress protein and the beta-flap of the bacterial core RNA polymerase. This activation event contrasts with the established mechanism of inhibition in which glutamate, by virtue of its electrostatic properties, helps to inhibit binding to ribosomal promoters after osmotic shock. Overall, Escherichia coli survival in natural hosts and reservoirs is expected to rely on the accumulation of simple ions that trigger changes in protein conformation that lead to global changes in transcription.
MeSH term(s)	DNA-Directed RNA Polymerases/antagonists & inhibitors ; DNA-Directed RNA Polymerases/chemistry ; DNA-Directed RNA Polymerases/genetics ; DNA-Directed RNA Polymerases/metabolism ; Enzyme Activation/genetics ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Osmolar Concentration ; Sigma Factor/antagonists & inhibitors ; Sigma Factor/chemistry ; Sigma Factor/genetics ; Sigma Factor/metabolism ; Transcriptional Activation/genetics ; Water-Electrolyte Balance/genetics
Chemical Substances	Escherichia coli Proteins ; Sigma Factor ; RNA polymerase Esigma(38) (EC 2.7.7.-) ; RNA polymerase sigma 70 (EC 2.7.7.-) ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2008-12-16
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/bi801075x
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Article: Control of the Timing of Promoter Escape and RNA Catalysis by the Transcription Factor IIB Fingertip

Tran, Khiem / Gralla, Jay D

Journal of biological chemistry. 2008 June 6, v. 283, no. 23

2008

Abstract	Transcription factor IIB (TFIIB) recruits RNA polymerase II to promoters and inserts a finger domain into its active site, with unknown consequences. Here we show that that the tip of this finger is important for two transcription initiation functions. First, TFIIB acts as a catalytic cofactor for initial RNA bond formation. It does so via a pair of fingertip aspartates that can bind magnesium, placing TFIIB within a family of proteins that insert finger domains to alter the catalytic functions of RNA polymerase. Second, the TFIIB fingertip mediates the timing of the release of TFIIB that is associated with appropriate promoter escape. These initiation requirements may assist in RNA quality control by minimizing functional synthesis when RNA polymerase becomes inappropriately associated with the genome without having been recruited there by TFIIB.
Language	English
Dates of publication	2008-0606
Size	p. 15665-15671.
Publishing place	American Society for Biochemistry and Molecular Biology
Document type	Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
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Article: Potassium glutamate as a transcriptional inhibitor during bacterial osmoregulation.

Gralla, Jay D / Vargas, David R

The EMBO journal

2006 Volume 25, Issue 7, Page(s) 1515–1521

Abstract: Potassium glutamate accumulates upon hyper-osmotic shock and serves as a temporary osmoprotectant. This salt leads to transcriptional activation of sets of genes that allow the cell to achieve long-term adaptation to high osmolarity. The current ... ...

Abstract	Potassium glutamate accumulates upon hyper-osmotic shock and serves as a temporary osmoprotectant. This salt leads to transcriptional activation of sets of genes that allow the cell to achieve long-term adaptation to high osmolarity. The current experiments show that potassium glutamate also acts as an inhibitor of bulk cellular transcription. It can do so independent of the involvement of macromolecular repressors or activators by virtue of its ability to directly inhibit RNA polymerase binding to ribosomal promoters. Thus, potassium glutamate mediates a global transcription switch by acting differentially on RNA polymerase at sets of genomic promoters that differ in their built-in direct response to this salt.
MeSH term(s)	DNA-Directed RNA Polymerases/genetics ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli K12/drug effects ; Escherichia coli K12/physiology ; Glutamates/pharmacology ; Osmotic Pressure ; Potassium Acetate/pharmacology ; Promoter Regions, Genetic ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; Ribosomes/genetics ; Ribosomes/metabolism ; Transcription, Genetic ; Water-Electrolyte Balance
Chemical Substances	Glutamates ; RNA, Bacterial ; RNA, Ribosomal ; DNA-Directed RNA Polymerases (EC 2.7.7.6) ; Potassium Acetate (M911911U02)
Language	English
Publishing date	2006-04-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.1038/sj.emboj.7601041
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Article ; Online: Stimulation of the XPB ATP-dependent helicase by the beta subunit of TFIIE.

Lin, Yin C / Gralla, Jay D

Nucleic acids research

2005 Volume 33, Issue 9, Page(s) 3072–3081

Abstract: TFIIE and TFIIH are essential for the promoter opening and escape that occurs as RNA polymerase II transits into early elongation. XPB, a subunit of TFIIH, contains an ATP-dependent helicase activity that is used in both of these processes. Here, we show ...

Abstract	TFIIE and TFIIH are essential for the promoter opening and escape that occurs as RNA polymerase II transits into early elongation. XPB, a subunit of TFIIH, contains an ATP-dependent helicase activity that is used in both of these processes. Here, we show that the smaller beta subunit of TFIIE stimulates the XPB helicase and ATPase activities. The larger alpha subunit can use its known inhibitory activity to moderate the stimulation by the beta subunit. Regions of TFIIE beta required for the helicase stimulation were identified. Mutants were constructed that are defective in stimulating the XPB helicase but still allow intact TFIIE to bind and recruit XPB and TFIIH to form the pre-initiation complex. In a test for the functional significance of the stimulatory effect of TFIIE beta, these mutant forms of TFIIE were shown to be defective in a transcription assay on linear DNA. The data suggest that the beta subunit of TFIIE is an ATPase and helicase co-factor that can assist the XPB subunit of TFIIH during transcription initiation and the transition to early elongation, enhancing the potential diversity of regulatory targets.
MeSH term(s)	Adenosine Triphosphatases/metabolism ; DNA Helicases/metabolism ; DNA-Binding Proteins/metabolism ; HeLa Cells ; Humans ; Mutation ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Protein Subunits/genetics ; Transcription Factors, TFII/chemistry ; Transcription Factors, TFII/genetics ; Transcription Factors, TFII/physiology ; Transcription, Genetic
Chemical Substances	DNA-Binding Proteins ; Protein Subunits ; Transcription Factors, TFII ; transcription factor TFIIE ; XPBC-ERCC-3 protein (146045-44-5) ; Adenosine Triphosphatases (EC 3.6.1.-) ; DNA Helicases (EC 3.6.4.-)
Language	English
Publishing date	2005-05-25
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gki623
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Article: Mechanism of stimulation of ribosomal promoters by binding of the +1 and +2 nucleotides.

Lew, Chih M / Gralla, Jay D

The Journal of biological chemistry

2004 Volume 279, Issue 19, Page(s) 19481–19485

Abstract: The rate of transcription of Escherichia coli ribosomal RNA promoters is central to adjusting the cellular growth rate to nutritional conditions. The +1 initiating nucleotide and ppGpp are regulatory effectors of these promoters. The data herein show ... ...

Abstract	The rate of transcription of Escherichia coli ribosomal RNA promoters is central to adjusting the cellular growth rate to nutritional conditions. The +1 initiating nucleotide and ppGpp are regulatory effectors of these promoters. The data herein show that in vitro transcription is also regulated by the +2 nucleotide. Both the +1 and +2 nucleotides act by driving polymerase into an altered conformation rather than by increasing the lifetime of transcription complexes. The unique design of the ribosomal promoters may stabilize a distorted state of polymerase that is relieved by the binding of the two nucleotides required for transcription initiation.
MeSH term(s)	Binding Sites ; DNA/chemistry ; DNA-Directed RNA Polymerases/chemistry ; Dose-Response Relationship, Drug ; Escherichia coli/metabolism ; Gene Expression Regulation, Bacterial ; Heparin/pharmacology ; Kinetics ; Nucleotides/chemistry ; Plasmids/metabolism ; Promoter Regions, Genetic ; Protein Conformation ; RNA, Ribosomal/chemistry ; Ribosomes/genetics ; Ribosomes/physiology ; Transcription, Genetic
Chemical Substances	Nucleotides ; RNA, Ribosomal ; Heparin (9005-49-6) ; DNA (9007-49-2) ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2004-03-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M401285200
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